In recent years, the global logistics industry has seen a growing demand for efficient port operation scheduling, especially in the context of intermodal transportation, where ports serve as critical logistics nodes, making their scheduling increasingly complex. Digital twin technology, by integrating physical ports with digital models, provides a new approach to optimizing scheduling. This paper presents a digital twin-driven dynamic scheduling decision-making method for intermodal port operation, addressing the pain points in intermodal port practice. The study takes intermodal port operation dynamic scheduling as the research object and designs a digital twin model to provide decision support and platform support for improving the efficiency of intermodal port operation, optimizing resource allocation, and reducing cost and energy consumption. The experimental test has verified the effectiveness of digital twin technology in improving scheduling efficiency and optimizing resource allocation. The research results show that the digital twin model can significantly improve the efficiency of port joint scheduling and reduce the time and cost of cargo transportation.